jdahm

This information is over 2 years old. Information was current at time of publication.

Elsevier and Dryad: Cooperative Linking Between Articles and Data Sets

dryad Journal publisher Elsevier and the Dryad Digital Repository recently announced a new cooperative effort providing two-way links between their content. This reciprocal linking between Dryad and Elsevier’s ScienceDirect platform is currently available for 28 journals, including:

If an article’s associated data set is stored on Dryad, you can link directly to it from ScienceDirect by clicking on the “Data in DRYAD” button, under “Applications and tools” in the panel to the right of the article display. A link to the ScienceDirect article will likewise appear on the Dryad Web page for the data set(s). Access to the full-text article is only available if the University of Pittsburgh has a subscription to that journal. Dryad also provides a citation for the data set, including its Digital Object Identifier (DOI), a persistent link to the data set(s). To see an example of the two-way linking, visit:

  • A ScienceDirect article from the journal Gene
  • The associated data sets in Dryad

Dryad is a non-profit organization with members worldwide; its mission is to make the data sets underlying scientific/medical research publications more discoverable, reusable, and citable. Researchers can deposit large data sets in Dryad, using it to facilitate peer review or to comply with journal, funding organization, and institutional data policies. Dryad is integrated with several other publishers and their journals, including Heredity and PLoS Biology.

Reciprocal linking with Dryad ties in with Elsevier’s “Article of the Future” program, which aims to improve the format of the scientific research article. Elsevier similarly collaborates with numerous other repositories, including GEO (Gene Expression Omnibus) and ClinicalTrials.gov.

*Parts of this article were reprinted from the Elsevier and Dryad Implement Reciprocal Linking between Datasets and Published Research Articles press release.

~ Jeff Husted

This information is over 2 years old. Information was current at time of publication.

Lynda.com: For Online Computer and Technology Training

lyndaloginbuttonIf you need to learn how to design a Web site, create a Google app, or use a Microsoft Office or Adobe product, now you can learn anytime, anywhere with Lynda.com. Lynda.com is a University licensed, online computer and technology training provider offering a broad range of courses including: Access, PowerPoint, Drupal, C++, and many more. The video-based courses are self-paced, up to several hours long, and divided into 5-15 minute lessons. Each course is taught by a subject expert. You can select from over 1,200 courses.

Lynda.com is available to all University of Pittsburgh users. Log in using your University Computer Account at my.pitt.edu. Mobile access is available for the iPhone, iPod touch, and Android mobile devices.

~ Jill Foust

This information is over 2 years old. Information was current at time of publication.

Treasures from the Rare Book Room: Horace Wells’ Letters

Horace Wells (1815-1848) was an American dentist who pioneered the use of nitrous oxide in tooth extractions. He was posthumously honored as the discoverer of modern anesthesia by the American Dental Association in 1864 and by the American Medical Association in 1870.

There was no greater promoter of Wells’ contribution than his main biographer, W. Harry Archer (1905-1980)—alumnus of the University of Pittsburgh, lecturer in the School of Dentistry, and later the head of the department of oral surgery of his Alma Mater. During his years at Pitt, with the support of Dean H. Edmund Friesell, Archer helped to build an outstanding collection on the discovery of anesthesia that primarily focused on Horace Wells. The collection included letters, instruments for delivering anesthesia, portraits, books, journals, and pamphlets. This collection of “Wellsiana” was the most complete in the country at that time, and the Wells family letters were its highlight. Archer obtained the letters for the collection from Mrs. Arthur Cole and from Miss Wales, relatives of Horace Wells.

During the reorganization of the dental school library in the 1970s, the collection’s anesthetic armamentarium and miniature portraits were donated by Archer to The Smithsonian.

The book I Awaken to Glory, in Falk Library’s Historical Collection, mistakenly spread the message that the whereabouts of the original letters collected by W. Harry Archer were unknown.1

Wells LettersHowever, these Wells family letters brought to Pittsburgh by Archer never left the University. Today, they are housed in the Rare Books and Special Collections of Falk Library, where they are properly cared for and stored in a climate controlled room. The letters can be viewed in our Rare Book Room by appointment. A finding aid is available.

1. Leonard F. Menczer and Richard J. Wolfe, eds. I Awaken to Glory: Essays Celebrating the Sesquicentennial of the Discovery of Anesthesia by Horace Wells, December 11, 1844–December 11, 1994 (Boston, Mass.: Boston Medical Library in the Francis A. Countway Library of Medicine, in association with the Historical Museum of Medicine and Dentistry, Hartford, Conn., 1994).

~ Gosia Fort

This information is over 2 years old. Information was current at time of publication.

HSLS Staff News

The HSLS Staff News section includes recent HSLS presentations, publications, staff changes, staff promotions, degrees earned, etc.

Publications

Rebecca Abromitis, reference librarian, along with co-authors Mei Song1, Kaihong Liu1, and Titus L. Schleyer1, published “Reusing Electronic Patient Data for Dental Clinical Research: a Review of Current Status” in Journal of Dentistry, 18 April 2013. [Epub ahead of print]

1. Center for Dental Informatics, Department of Dental Public Health, University of Pittsburgh School of Dental Medicine, Pittsburgh, PA 15261.

Jonathon Erlen, history of medicine librarian, published “Dissertations Recently Completed in Related Fields” in Journal of the History of Sexuality, 22(3): 554-5, 2013.

Presentations

Kate Flewelling, outreach coordinator, National Network of Libraries of Medicine, presented two talks, “Bridges Cost Money: Finding Grant Opportunities” and “Promoting Environmental Health Education: Free Resources from the National Library of Medicine,” at the Joint Council of Extension Professionals, Galaxy IV Conference in Pittsburgh, Pennsylvania on September 17-19, 2013.

This information is over 2 years old. Information was current at time of publication.

Classes October 2013

HSLS offers classes on database searching, software applications such as Adobe Photoshop, bibliographic management, molecular biology and genetics, and library orientations. For more information, visit the online course descriptions.

Classes are held on the first floor of Falk Library (200 Scaife Hall) in Classroom 1 and on the upper floor of the library in Classroom 2. All classes are open to faculty, staff, and students of the schools of the health sciences at the University of Pittsburgh. They are also open to UPMC residents and fellows.

Faculty, staff and students of the schools of the health sciences will need a valid Pitt ID or e-mail account to attend these classes. UPMC residents/fellows will need to show their UPMC IDs.

No registration is required, except where noted. Seating for classes is first-come, first-served, until the class is full. Classes marked with an asterisk (*) qualify for American Medical Association Category 2 continuing education credit.

Class schedules are subject to change. Please consult the online class calendar for the most current information.

HSLS CLASSES

Adobe Photoshop (Falk Library Classroom 2)

Tuesday, October 1 Noon-2 p.m.

Advanced PowerPoint for Presentations (Falk Library Classroom 2)

Tuesday, October 22 1-3 p.m.

Data Management Plans (102 Benedum Hall)

Registration required

Wednesday, October 30 Noon-1 p.m.

EndNote Basics (Falk Library Classroom 2)

Wednesday, October 23 10 a.m.-noon

Introduction to HSLS Resources and Services at Falk Library
(Meet inside entrance to Library)
Offered upon request to groups or individuals. Call 412-648-8866.

NIH Public Access Policy Compliance Boot Camp (Falk Library Classroom 1)

Thursday, October 3 Noon-1 p.m.
Thursday, October 17 Noon-1 p.m.
Thursday, October 31 Noon-1 p.m.

Prezi for Presentations (Falk Library Classroom 2)

Tuesday, October 29 1-3 p.m.

Undead PubMed* (Falk Library Classroom 1)

Thursday, October 10 10-11 a.m.
Wednesday, October 16 9-10 a.m.
Tuesday, October 22 2-3 p.m.
Thursday, October 31 3-4 p.m.

MOLECULAR BIOLOGY AND GENETICS RESOURCES

Personal Genomics* (Falk Library Classroom 2)

Wednesday, October 2 1-3 p.m.

Microarray Data Analysis* (Falk Library Classroom 2)

Wednesday, October 9 1-3 p.m.

Genome Browsers* (Falk Library Classroom 2)

Wednesday, October 16 1-3 p.m.

Gene Regulation Resources* (Falk Library Classroom 2)

Wednesday, October 23 1-3 p.m.

Cancer Informatics* (Falk Library Classroom 2)

Wednesday, October 30 1-3 p.m.

POSTDOC TALKS

Choosing the Best 3D Matrix for Your Cell Culture Needs (Falk Library Classroom 2)

Tuesday, October 1 3-4:30 p.m.

How to Prepare a CV (grad students & postdocs) (Falk Library Classroom 2)

Thursday, October 10 Noon-1:30 p.m.

Adding Mechanistic Insight through Signal Transduction Research (Falk Library Classroom 2)

Thursday, October 17 10-11:30 a.m.

How to Process Histology Images in Photoshop-the Basics (Falk Library Classroom 2)

Friday, October 25 1:30-3:30 p.m.

CUSTOMIZED CLASSES

Customized classes can be developed for your department, course, or other group.

FLASHCLASS

FlashClass is a “deal of the week” Groupon-like offer of timely and useful learning. Each week’s offer proposes one or two topics, and you’re invited to sign up to attend a one-hour class the following week. If at least three people sign up, we’ll hold the class. (We’ll notify you either way.)

This information is over 2 years old. Information was current at time of publication.

“Life and Limb: The Toll of the American Civil War” Coming to Falk Library on September 16

The Civil War was a turning point in American history, and now you can explore this fascinating period of time through the National Library of Medicine (NLM) exhibit, “Life and Limb: The Toll of the American Civil War,” which opens September 16 at Falk Library. The exhibit focuses on disabled veterans and their role as symbols of the fractured nation.

Veterans John J. Long, Walter H. French, E. P Robinson, and an unidentified companion, 1860s Courtesy Library of Congress
Veterans John J. Long, Walter H. French, E. P. Robinson, and an unidentified companion, 1860s
Courtesy Library of Congress

Topics presented will include: Continue reading →

This information is over 2 years old. Information was current at time of publication.

Introducing ClinicalKey (and Farewell to MD Consult)

ClinicalKey LogoClinicalKey is the new clinical reference resource from Elsevier and the replacement for MD Consult. Elsevier developed ClinicalKey around three key requirements—comprehensiveness, trusted content, and speed to answer—which they identified in a study of over 2,000 physicians. As with MD Consult, ClinicalKey offers access to multiple content types—including e-books, journals, videos, and images—from a single interface. However, the breadth of content in ClinicalKey is far greater:

Content Type

ClinicalKey

MD Consult

E-books

1,100+

89

Journals

575+

54

Videos

13,000+

3,600

Images

5,000,000+

50,000+

In addition, ClinicalKey includes a wider collection of the Clinics series, as well as First Consult, Elsevier’s evidence-based point-of-care tool.

A sample results page from a search for “viral hepatitis” is shown below:ClinicalKey

Pointing your mouse at a search result in the center panel will reveal a double arrow. Click on the arrow to preview the content in the right panel—without losing your search results list. To view the full content, click on the title of the search result.

Need images for a presentation? You can drag and drop image results to the Presentation button, or you can select images from the results list by clicking on the check boxes and then clicking on the “+” sign next to the Presentation button. Click the Presentation button to open the Presentation Maker, where you can organize images and export them to PowerPoint.

You will need to create a personal ClinicalKey account to fully use the Presentation Maker, as well as save searches, create a reading list, or earn CME credit.

Need some time to transition? ClinicalKey is available now, but MD Consult will remain available until November 30, 2013.

For more information, contact the HSLS Main Desk at 412-648-8866 or Ask a Librarian.

*Parts of this article were derived from the ClinicalKey promotional flyer and quick reference card.

~ Jeff Husted

This information is over 2 years old. Information was current at time of publication.

DSM-5 Now Available

HSLS now provides access to the online version of DSM-5, the latest revision of the Diagnostic and Statistical Manual of Mental Disorders. Published by the American Psychiatric Association (APA), the DSM is considered the authoritative guide to diagnosing mental disorders. The last major revision (DSM-IV) was published in 1994, with a text revision (DSM-IV-TR) in 2000.

David J. Kupfer, MD, Thomas Detre Professor of Psychiatry, chaired the task force that oversaw the development of DSM-5. Between 2008 and 2012, the DSM-5 Task Force and thirteen Work Groups drafted, revised, and finalized the diagnostic criteria and text of DSM-5. More than 160 members of the task force and work groups reviewed the research literature, analyzed data, sought feedback from colleagues, and organized field trials. DSM-5 was officially released in May 2013.

The APA aimed to develop DSM-5 as an evidence-based manual: “Decisions to include a diagnosis in DSM-5 were based on a careful consideration of the scientific advances in research underlying the disorder, as well as the collective clinical knowledge of experts in the field.”1 In addition, many of the changes in DSM-5 attempt to address symptoms and behaviors that were not well defined by DSM-IV.1

To access the online version of DSM-5:

  1. Search DSM-5 in the Pitt Resources Quick Search box.
  2. Visit the Psychiatry section on the Health Sciences E-Books by Subject Web page.

More information about DSM-5 is available from these APA Web sites:

A print copy is also available at the Falk Library Main Desk.

1. “About DSM-5/Frequently Asked Questions,” American Psychiatric Association, accessed July 31, 2013, http://www.dsm5.org/about/Pages/faq.aspx.

~ Jeff Husted

This information is over 2 years old. Information was current at time of publication.

Postdoc Talks: A New “How to” Training Series

The HSLS Molecular Biology Information Service (MBIS) and the Center for Postdoctoral Affairs in the Health Sciences are pleased to announce a new workshop series taught by postdoctoral associates at the University of Pittsburgh.

The inaugural series features six postdoctoral instructors from the Departments of Neurobiology, Cell Biology, Urology, and Obstetrics, Gynecology, and Reproductive Sciences. Workshops will be held in Falk Library, Classroom 2.

Schedule of upcoming workshops:

Monday, September 9, 10:30 a.m.-noon  

Teresa Liu will present, “DNA/RNA Immunoprecipitation and Next Generation Sequencing.”

Tuesday, September 17, 1-2:30 p.m.                   

Tejas Tirodkar will present, “How to Process Histology Images in Photoshop—the Basics.”

Tuesday, October 1, 3-4:30 p.m.              

Lisa Gurski will present, “Choosing the Best 3D Matrix for Your Cell Culture Needs.”

Thursday, October 10, noon-1:30 p.m.           

Emily Wickline will present, “How to Prepare a CV (Graduate Students and Postdocs).”

Thursday, October 17, 10-11:30 a.m.                    

Ethan Block will present, “Adding Mechanistic Insight through Signal Transduction Research.”

If you are a postdoc interested in teaching a “how to” workshop during the next series, please contact Carrie Iwema by e-mail at iwema@pitt.edu. The MBIS works with postdocs to create a workshop that is both a positive teaching experience and instructive to attendees. All postdoc instructors receive feedback and a letter of acknowledgement. Participating postdocs acquire valuable instructional experience while providing a service to our health sciences community.

~ Carrie Iwema

This information is over 2 years old. Information was current at time of publication.

Happy New Year!

We are pleased to welcome new and returning faculty, staff, and students. Although the new calendar year officially begins in January, August begins the new academic year. There are a few things you should know about the library that can make this new year easier for you:

We invite you to use the library’s resources and services to support your teaching, learning, and research activities. Have a great year!

~ Nancy Tannery

This information is over 2 years old. Information was current at time of publication.

Need Nursing and Allied Health Information? CINAHL has an App for That!

Are you a nurse or physical therapist trying to use your mobile device to conduct research? Access the CINAHL database, via the EBSCOhost app, to locate journal articles, books, and conference proceedings related to nursing and allied health fields. The app is available to Pitt and UPMC users through the HSLS subscription to the full CINAHL database.

Compatible Devices

The EBSCOhost app is free to download and is available for the iPhone/iPad from the iTunes App store (iOS 3.0 or later required) and for Android devices from Google Play (Android 2.1 or later required).

Getting Started

An authentication key is required to use this app. To obtain the key:

  1. Direct your browser to CINAHL.
  2. Scroll to the bottom of the page and then click on iPhone and Android apps.
  3. Enter your e-mail address and then click on Send.
  4. Access your e-mail from your mobile device and follow the instructions. If the EBSCOhost app has not yet been downloaded on your device, a link will be provided to do so.

Once the app is authenticated, it can be used for nine months, after which you must send yourself a new authentication key from the EBSCOhost interface by repeating the above instructions.

CINAHLApp Features

  • Search using keywords, subject headings, or author name.
  • Save your searches and citations.
  • Send articles via e-mail.
  • Limit your results by full-text PDF availability, date range, or articles from peer-reviewed journals.

Limitations

The app does not provide full-text access to all articles available through HSLS subscriptions; it only links directly to selected full-text articles available in PDF. Also, the full version of the CINAHL database allows additional limits such as inpatients, outpatients, and pregnancy.

For more information about the CINAHL database, via the EBSCOhost app, or other mobile friendly versions of HSLS resources, such as Micromedex and AccessMedicine, direct your browser to the HSLS Mobile Resources Web site.

~ Melissa Ratajeski

This information is over 2 years old. Information was current at time of publication.

Data Management Planning: Data Sharing

Data sharing is an important part of the scientific method. The University of Pittsburgh’s Guidelines on Data Management aligns with the National Institutes of Health (NIH) and the National Science Foundation (NSF) policies stating that data developed with federal funds should be shared on request with other researchers. With federal budgets under increasing pressure, data sharing leverages public investment by:

  • Speeding discovery
  • Making available unique and difficult to replicate data
  • Enabling the exploration of new topics
  • Eliminating redundancy
  • Facilitating validation studies
  • Discouraging fraud
  • Permitting the creation of new data sets by combining data from multiple sources
  • Facilitating meta-analysis
  • Encouraging diversity of analysis and opinion

Additionally, publishers such as Nature, Science, and PLoS require that supporting data be made available as a condition of publication, in turn making data more easily found online via data repositories. Benefits to researchers include increased publication citation1 rates, access to new research data, and convenient long-term storage.

What is research data?

When meeting the requirements of the NIH and NSF, data is not simply what appears in the published article: it is the “recorded factual material…necessary to validate researching findings,”2 i.e., the raw data on which summary statistics and tables are based. The University of Pittsburgh further classifies research data3 as intangible (statistics, findings or conclusions) or tangible (notebooks, videos, forms, etc.).

Is there a timeline for sharing data?

NIH mandates that final research data be shared “no later than the acceptance for publication of the main findings from the final data set.”4 Describe plans in the NIH data management plan (DMP),5 required for projects seeking $500,000 or more in direct costs in any year. The DMP is a brief paragraph following the Research Plan of the application, and does not count towards the page limit.

NSF requires sharing final research data for all projects in a “reasonable length of time6 as long as the cost is modest.” The NSF DMP5 is two pages maximum for all full proposals, and does not count towards the 15-page Project Description.

“Data Repositories: Meeting Your Research Needs” will be covered in a future article.

1. H.A. Piwowar, R.S. Day, D.B. Fridsma, “Sharing Detailed Research Data Is Associated with Increased Citation Rate,” PLoS One 3, no. 3 (2007):e308.

2. U.S. Office of Management and Budget, Executive Office of the President, Federal Register Notice re OMB Circular A-110 (Washington, D.C., September 30, 1999), http://www.whitehouse.gov/omb/fedreg_a110-finalnotice.

3. University of Pittsburgh, Guidelines on Research Data Management (Pittsburgh, PA, November 25, 2009), http://www.provost.pitt.edu/documents/RDM_Guidelines.pdf.

4. National Institutes of Health (NIH), Final NIH Statement on Sharing Research Data (Bethesda, MD, February 26, 2003), http://grants.nih.gov/grants/guide/notice-files/NOT-OD-03-032.html.

5. National Institutes of Health (NIH), NIH Data Sharing Policy and Implementation Guidance (Bethesda, MD, February 9, 2012), http://grants.nih.gov/grants/policy/data_sharing/data_sharing_guidance.htm .

6. National Science Foundation, Biological Sciences Directorate, Information about the Data Management Plan Required for all Proposals (2/20/13) (Arlington, VA, February 20, 2013), http://www.nsf.gov/bio/pubs/BIODMP061511.pdf.

~ Andrea Ketchum

This information is over 2 years old. Information was current at time of publication.

Next.Data.gov

Next.Data.gov is a “very early” preview of the redesign of DATA.gov. The goal of Next.Data.gov is to make federal government metadata resources more transparent and easy to use as mandated by President Obama’s May 2013 Open Data Executive Order.

Currently, DATA.gov provides over 75,000 data sets from federally funded studies, projects, and information. President Obama noted in his sneak preview announcement that “data [is available] on everything from what different hospitals charge for different procedures, to credit card complaints, to weather and climate measurements.” The data sets in DATA.gov come from numerous participating federal agencies, departments, and organizations.

Next.Data.gov will begin to index data sets from agencies that publish their data catalogs publicly. This early preview features data sets from the Department of Health and Human Services, one of the first federal agencies to publish a machine-readable version of its data catalog.

The collection of health-related data includes:

  • FDA recalls and safety alerts
  • Public health data
  • Health indicators
  • Clinical trials
  • Hospital quality data
  • Medicare plans
  • And more…

A design feature of Next.Data.gov includes streams of blog posts, tweets, and quotes that illustrate how companies and the public use federal metadata. The responsive design allows the core content to adjust to the screen size of a smartphone or tablet.

NextDataGov

Next.Data.gov makes note to tell users that it is still in beta and asks for feedback via Twitter and Quora.

For more information about Next.Data.gov, direct your browser to the White House announcement, “First Look at Next.Data.gov.”

~ Charlie Wessel

This information is over 2 years old. Information was current at time of publication.

HSLS Staff News

The HSLS Staff News section includes recent HSLS presentations, publications, staff changes, staff promotions, degrees earned, etc.

Publications

Jonathon Erlen, history of medicine librarian, along with Jay Toth, published, “American Indian Dissertation Abstracts” in Indigenous Policy Journal 24, no. 1 (Summer 2013).